Journal
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
Volume -, Issue 147, Pages -Publisher
JOURNAL OF VISUALIZED EXPERIMENTS
DOI: 10.3791/59219
Keywords
Biochemistry; Issue 147; Mass spectrometry; microbiology; natural products; specialized metabolites; MALDI-TOF MS; bioinformatics
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Funding
- National Institute of General Medical Sciences [R01 GM125943]
- National Geographic Grant [CP-044R-17]
- Icelandic Research Fund [152336-051]
- University of Illinois at Chicago startup funds
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In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.
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